A "clipper", as I understand it, is orbiting a planet to repeatedly flyby one of its moons. Mariner 10 orbited the Sun to fly by Mercury 3 times. Should clippers in general use retrograde orbits in order to get more frequent flybys (or "clips")? Or are instead slower flybys prefered?
The purpose of most missions are to study planetary bodies in detail, taking images, using radar or lasers for ranging and mapping, using gravimetric instruments to measure composition, etc. All these types of activities benefit from slower relative movement between the spacecraft the the body being studied.
There may be some mission profiles where more frequent flybys would be better than longer lasting flybys, although I can't think of any at the moment. Of course it may be that fuel limitations would mean that only a retrograde orbit is possible, in which case you take what you can get.